Complete sequencing of ape genomes

2025/04/09 by DongAhn Yoo, Arang Rhie, Prajna Hebbar +97 · 1 voice · 130 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Psychology · #Biological evolution #Biology #Centromere #Chromosomal and Genetic Variations #Chromosome #Comparative genomics #Evolutionary biology #Gene #Genetics #Genome #Genomics #Genomics and Phylogenetic Studies #Gorilla #Heterochromatin #Hominidae #Lineage (genetic) #Primate Behavior and Ecology #Segmental duplication #Telomere

paper · pdf · doi:10.1038/s41586-025-08816-3

published in Nature 641(8062), 401-418 (Nature Portfolio)

openalex publication_date 2025/04/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06

Abstract

. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.

Citations

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Cited by

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• Not Just N_e N_e-more: New Applications for SMC from Ecology to Phylogenies
• Non-canonical DNA in human and other ape telomere-to-telomere genomes
• Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats
• Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life
• The formation and propagation of human Robertsonian chromosomes
• Unique and divergent features of human brain development
• Substitution Spectrum and Selection at G-quadruplexes in Great Ape Telomere-to-Telomere Genomes
• Mammalian mitochondrial DNA accumulates insertions and deletions with age in energetically demanding tissues
• The repertoire of short tandem repeats across the tree of life
• A new super-pangenome pipeline reveals domestication signatures of conserved noncoding sequences in the orange subfamily
• Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring
• A global map for introgressed structural variation and selection in humans
• In Vitro Massively Parallel Screening of Human Regulatory Elements Involved in Postcranial Skeletal Development for Differential Activity Compared to Chimpanzee
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• Complex Genomic Structural Variation Underlies Climate Adaptation across Eucalyptus species
• FastGA: Fast Genome Alignment
• VAMPIRE: Analyzing variation and motif pattern in tandem repeats
• Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes
• A global view of human centromere variation and evolution
• Supregraph: Enabling Information-Optimal Assembly Graph Representation of a Read Set
• Non-canonical DNA in human and other ape telomere-to-telomere genomes. [europepmc]
• Highly accurate assembly polishing with DeepPolisher. [europepmc]
• Comparative Analysis of Mammalian Adaptive Immune Loci Revealed Spectacular Divergence and Common Genetic Patterns. [europepmc]
• Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower (Mimulus guttatus) Complex. [europepmc]
• The formation and propagation of human Robertsonian chromosomes. [europepmc]
• Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes. [europepmc]
• Long-read sequencing of primate testis and human sperm allows identification of recombination events in individuals. [europepmc]
• Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies. [europepmc]
• JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes. [europepmc]
• Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation. [europepmc]
• Satellite DNA Genomics: The Ongoing Story. [europepmc]
• Multispecies pangenomes reveal a pervasive influence of population size on structural variation. [europepmc]
• The repertoire of short tandem repeats across the tree of life. [europepmc]
• Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium . [europepmc]
• Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats. [europepmc]
• Substitution Spectrum and Selection at G-quadruplexes in Great Ape Telomere-to-Telomere Genomes. [europepmc]
• Finding low-complexity DNA sequences with longdust. [europepmc]
• Genetic diversity and regulatory features of human-specific NOTCH2NL duplications. [europepmc]
• Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life. [europepmc]
• Germline sequence variation within the ribosomal DNA is associated with human complex traits. [europepmc]
• Modular genetic architecture underlies human hand and foot evolution. [europepmc]
• Duplicate, diversify, repeat: The evolution of NOTCH2NL. [europepmc]
• Complete chromosome 21 centromere sequencing of families with Down syndrome. [europepmc]
• MGA: a tool for haplotype-mixed assembly of long and accurate reads. [europepmc]
• A global view of human centromere variation and evolution [europepmc]

Discussions

• A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... [bsky, 155 points, 5 comments]

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